All the indicted officers have been suspended without pay and had their guns taken away, Police Chief Greg Suhr said shortly after the indictments were announced.
"Our department is shaken. This is as serious as an issue as I can recall in my time in the department," said an emotional Suhr, who has been with the department since 1981.
Suhr said federal authorities assured him the arrests did not reflect a systemic problem in the department.
Furminger, Robles and Vargas each face counts of drug conspiracy and drug distribution that each carries a maximum possible sentence of 20 years in prison and a $1 million fine. They also face a charge of civil rights conspiracy that carries a sentence of up to 10 years and a $250,000 fine, and a federal program theft charge.
Vargas pleaded not guilty Thursday and was released on $50,000 bond. The other defendants were expected to make a court appearance Friday.
In a separate indictment, three other defendants were charged with civil rights violations that prosecutors said involve illegally entering hotel rooms and intimidating occupants.
The charges were based on surveillance footage from a hotel in the Tenderloin neighborhood that was released by the city's public defender, Jeff Adachi, in 2011. Adachi claimed the videos of plainclothes officers contradicted police reports and sworn police testimony.
Officer Arshad Razzak, 41, and Officer Richard Yick, 37, both of San Francisco; and Officer Raul Eric Elias, 44, of San Mateo each face three civil rights charges that carry possible penalties of up to 10 years in prison and a $250,000 fine.
The indictment did not provide additional detail about the searches.
However, a civil lawsuit filed by three occupants of Hotel Henry in 2012 claimed Razzak, Elias, and three other officers got the hotel's master key and forced their way into rooms without a search warrant or the occupants' consent on two separate occasions. They searched the occupants and the room then made drug arrests, the lawsuit states.
A judge concluded that video evidence contradicted the officers' testimony, and criminal charges against the defendants were dismissed, the suit says.
The defendants sued the arresting officers and police department. The Board of Supervisors approved a $150,000 settlement in December.
In the current case, Razzak and Yick have also been charged with falsifying police reports.
None of the defendants in either indictment could be reached for comment.